Tag Archives for PCR

psgurel – I’ve just spent most of my morning in lab meeting, and will spend my afternoon going to a few lectures. Presenting work and getting feedback is a critical part of science. Lab meetings are somewhat more informal sessions where the entire lab can get together and discuss specific details on members’ projects. It’s helpful for all involved in terms of troubleshooting, fine tuning direction of the research project, etc. It’s fun, but can also be somewhat tiring. Here’s my post lab meeting selfie 🙂

crestwind24 – This morning I came into lab very early to make sure I got all of my experiments done before heading to Philadelphia in the afternoon. One of the things I needed to do was run 4 PCR reactions and then image the products of the reactions using gel electrophoresis. Or more simply, I needed to make specific fragments of DNA from the C. elegans genome, and then make sure I made the correct DNA by looking at its size. When I visualized the PCR reactions separated by size on an agarose gel (top panel), I did not see the size DNA I was making with the PCR. Instead I saw a bunch of randomly sized bands and smears (hence my grumpy face when sitting at the gel imager, bottom left). Luckily, since I was in lab so early, I redid the PCR at a different temperature and got nice crisp bands at the exact size I expected (right bottom panel)!!! I love when molecular biology works!!!

More than 20,000 people have been diagnosed with Ebola virus and more than 7,800 have died of it, according to the latest data from the World Health Organization. It’s a new milestone in the ever-worsening Ebola epidemic in Sierra Leone, Liberia and Guinea, and it shows Sierra Leone has more cases than any other country.

crestwind24: Today I am doing PCR to amplify a gene I am interested in from the DNA of a worm (C. elegans). PCR, or Polymerase Chain Reaction, can be used to make DNA, check for the presence of DNA, and/or sequence DNA. PCR is commonly used to detect the presence of viruses, like Ebola, by looking for the DNA of the virus in the patient’s blood or bodily fluids. Setting up a PCR involves pipetting small volumes of liquid, containing DNA, enzymes, salts, etc into tiny tubes (see images). Then the tubes are placed into a cycling machine (ours is named Cycle Jackson… get it?) that changes temperature over and over in a cycle to activate the enzyme that makes the DNA. At the end I hopefully will have a bunch of the DNA I want!

psgurel: Today I am staining grids for Negative StainElectron Microscopy. I will be using the TEM (Transmission Electron Microscope) which essentially uses a high voltage electron beam to visualize samples. My samples are placed on tiny grids (the arrow in my picture) and then stained with uranyl acetate, which is slightly radioactive (hence why I have to wear a lab coat) and scatters the electron beam. As a result, my samples stained with uranyl acetate will not absorb electrons and thus I can visualize them in contrast to the grid surface which will absorb electrons. Why use TEM instead of other types of microscopy? A typical fluorescence microscope yields about 200nm resolution. However, I’m trying to visualize protein clusters of less than 100nm in length…about 10,000x smaller than a grain of sand! The TEM will be able to resolve these structures!

The method takes about 30 minutes or less and can be conducted in rural areas where there are no power cables, said Jiro Yasuda, professor of infectious diseases at Nagasaki University, today. The technique, initially reported in 2007 in Journal of Virological Methods by Yasuda and his colleagues, was modified to be used for the strain of Ebola that’s blamed for more than 1,550 deaths in West Africa.

The World Health Organization has just confirmed that the newly-identified cases of Ebola Virus Disease (EVD) in the Democratic Republic of Congo is genetically unrelated to the strain currently circulating in Liberia, Guinea, Sierra Leone, and Nigeria.

A WHO collaborating research center in Franceville, Gabon, the Centre International de Recherches Médicales, had previously identified six Ebola positive samples sent to the laboratory. They report today that, “the virus in the Boende district is definitely not derived from the virus strain currently circulating in west Africa.”